As G.I. Joe sets up their base of operations on the U.S.S. Flagg, on Delta Space Station, Dusty and Mutt warn the team about Cobra's plan to plant cubes at strategic locations in order to create the pyramid of darkness. Shipwreck and Snake Eyes travel underneath Enterprise City with secret control cubes, while the rest of the Joes plans to stop Destro from activating the first cube at the "Devil's Playground".
Tomax is captured by G.I. Joe, causing his identical twin brother Xamot to plan on rescuing him before Cobra can activate the final cube in the "Sea of Lost Souls". Shipwreck and Snake Eyes find an ally in a pop singer named "Satin", who helps them escape Cobra's troopers in Enterprise City.
Cobra activates the Pyramid of Darkness, leaving the Joes stranded at sea. The Crimson Twins anticipate Cobra Commander's treachery and signal for the Dreadnoks to relieve Zartan and Cobra Commander of control. Alpine and Bazooka ally with Quick Kick, a stuntman and karate expert from Hollywood.
G.I. Joe regains control of Space Station Delta, and they launch a full-scale assault on Cobra Temple, destroying the control cubes and the Pyramid of Darkness.
Cobra tries to attack a global anti-terrorism conference when they send Zartan to replace an ambassador and blow up the Worldwide Defense Center, but G.I. Joe captures and places him in the Defense Center's prison.
Roadblock's aunt and uncle run a fast food place called Red Rocket owned by Extensive Enterprises, Cobra's business alias. The rocket design hides extremely destructive warheads that Cobra hopes to utilize. G.I. Joe goes on a countrywide search for Red Rocket restaurants with Cobra missiles.
A military satellite crashes into the South Pacific, causing a race between G.I. Joe and Cobra to gain possession of it. A primitive tribe finds it first, claiming it as their god.
Cobra uses a cloaking device to make oil tankers disappear so they can detonate them by remote in an effort to take control of the world's fuel supply, unless G.I. Joe can stop the bombings.
In a plan to attack the world's cities with lava, Dr. Shakur, a scientist who invented the Vulcan Machine, is captured by Cobra. G.I. Joe must head into Cobra's jungle base, rescue the doctor and stop Cobra from carrying out their mission before these cities literally become "hotspots".
Cobra uses a special weapon called "Hi-Freq" given to them by an evil scientist named Dr. Lucifer, which a mind control device that takes over all animals in the animal kingdom, including Mutt's dog Junkyard. G.I. Joe has to stop Cobra's Hi-Freq device and save every animal in the world, especially Junkyard who isn't man's best friend, but Mutt's worst enemy.
Several scientists have been captured by Cobra and imprisoned in South America, prompting the Joes to rescue them and go through Cobra's booby-trapped "funhouse".
The Joes discover Cobra's plan to invade the Rocky Mountain Chemical Weapons Arsenal to possess explosive gas, all while under scrutiny from Hector Ramirez, host of the television show Twenty Questions.
A top secret nitrogen rocket fuel is stolen from the Joes and is accidentally stored in a greenhouse. The plants grow immensely, giving Destro a plan to seed the world with mutated fruits and vegetables to crush G.I. Joe in this gigantic jungle.
Cobra creates a weapon called the "Ion Attractor" that can pull down the Aurora Borealis to melt the polar icecaps and flood the world. G.I. Joe and a group of scientists must head north to prevent a global disaster.
Zartan makes constructs called synthoids, artificial beings or life forms loyal only to Cobra. Cobra makes Synthoids of Admiral Ledger, Colonel Sharp, General Franks, General Howe, and Duke to cut off G.I. Joe's resources and undermine morale.
Betrayed by an impostor in their ranks, G.I. Joe is disbanded by the government. Now fugitives from the military, the Joes must ally with Destro who gives them information on how to defeat Cobra Commander and Zartan to regain their resources.
Cobra Commander and the Baroness hire a Gypsy to summon three ghosts; a Centurion warrior, a Mongolian Amazon, and a World War I American pilot ace, to destroy G.I. Joe. The Baroness informs the Joes to locate a Roman coin, a wedding ring, and heart-shaped locket from Cobra Commander, and then bury the items to make the ghosts disappear.
Cobra Commander's personal Firebat with a homing signal was located at a Hollywood studio for a filming of "The G.I. Joe Story". Cobra hires Zartan and the Dreadnoks to recapture the Firebat before G.I. Joe can discover it and use the homing device to attack Cobra headquarters.
A sleazy political candidate hires Cobra to cause trouble for his opponent Robert Harper during their mayoral campaign race. They keep sending gang members to harass and ruin his campaign. But G.I. Joe is sent in to restore law and order.
Cobra invents a molecular degenerator to disrupt all U.S. currency, allowing them to mint their own Cobra money. The Joes must destroy the machine before Cobra can takes over the world with the face of Cobra Commander on every paper money.
Cobra captures people with psionic abilities in order to exploit their powers to rule the world and one of them is Airborne's telekinetic little brother.
Cobra steals all the gold bars from Fort Knox and loads it inside a bullet train. G.I. Joe plans on stopping the Cobra Bullet before it reaches the coast.
Cobra develops a powerful sound weapon and attacks a Sheik's oil supply with it in the Middle East. G.I. Joe must stop Cobra before they leak oil everywhere.
Wild Bill and a few Joes head to a farm in Texas to investigate a dude ranch Cobra captured, near the solar panels in order to control a nearby power station.
A twisted tycoon captures Flint, Lady Jaye, Baroness, and Cobra Commander, who must work together to escape the life size toys that are attacking them.
The Baroness spies on the Joes to gain access to the laser guidance system for Cobra Commander. While giving a martial art demonstration, Quick Kick meets Amber, a college student who dreams of being a Joe. They pair soon date and as his girlfriend, Amber gets closer to the Joes secrets, which causes them to think she is a Cobra spy.
Cobra steals a dangerous bacteria which causes a strong bacterium and growth serum to form a living germ monster that consumes everything in its path.
At his fire station, Barbecue keeps getting phone calls with cryptic messages from a man who calls himself "The Viper" and enlists the rest of the Joes to help him catch this mysterious man.
The Baroness uses the song of the Sirens to put the males under her evil spell. With their comrades under the Baroness' control, Cover Girl, Lady Jaye, and Scarlett are the only ones who can stop her and set their hypnotized friends free.
In an attempt to stop a world financial summit, Cobra heads to Japan to cause an artificially created earthquake that will destroy Tokyo unless G.I. Joe can stop their plans.
Cobra kidnaps family members of several G.I. Joe members and brainwashes them to obey the Baroness' commands. The Baroness commands the captives to attack the Joes in her attempt to retrieve the explosive crystals that Cobra created.
Scarlett and the other Joes set out to find a way to free their families from the Baroness' control. Unfortunately, the Baroness wants possession of the crystals and she would stop at nothing to get what she wants.
While camping, Bazooka sees a Cobra flight pod get "eaten" by a giant sea serpent. In reality, this "sea serpent" is a Cobra submarine planning to steal everything it devours. But when it goes out of control, the sea serpent goes on a rampage and the Joes must stop it from destroying New York.
G.I. Joe sets up a radar tracking station in England. While Storm Shadow finds King Arthur's legendary sword Excalibur at the bottom of a lake and uses its strength to attack the Joes and destroy their station.
During a struggle between G.I. Joe and Cobra, an accident triggers an experimental weapon. The Joes are plunged into unconsciousness. When they awaken, the explosion hurls them into an alternate reality, where Washington, D.C. and the rest of the world are under the control of Cobra.
While stuck in the alternate world, the Joes find an unlikely ally, the Baroness. Steeler learns that the Baroness of this world is a double agent and his beloved. She helps rescue the Joes and sends them back to their own home world. But Steeler, Clutch, and Grunt decide to stay in the other world after seeing what Cobra had done to their alternate selves.
Destro concocts a love potion out of Cleopatra's perfume for the Baroness to make a wealthy shipping tycoon fall in love with her. But things turn awry when Lady Jaye is sprayed with the scent.
Story by: Dann Thomas and Roy Thomas
It's Christmas Eve and most of the Joes have gone home for the holidays. After using special growth/shrinking ray and special toys (similar to the Trojan Horse) slipped into the donated toys for charity, Cobra ends up successfully infiltrating the G.I. Joe Headquarters, captures the Joes present, and rewires the Joes equipment. They plan on attacking Keystone City on Christmas to have residents believe the Joes have turned treacherous against them.
While in the midst of transporting valuables, G.I. Joe gets ambushed by Cobra, causing them to accidentally set a remote cabin in the mountains on fire. This makes the cabin's owner, Charlie Fairmont demand retribution against Cobra and Lady Jaye helps him with his revenge.
Gordon Kent
Cobra heads for Egypt to steal the treasure of Osiris in an underground tomb. G.I. Joe find themselves facing him and the Egyptian gods while Cobra faces Set, the Egyptian god of evil.
Cobra steals dinosaur bones and kidnaps a biologist to have him recreate the dinosaurs in a cloning device with rapid growth serum in order to destroy G.I. Joe and rule the world.
Flint visits his cousins in Pleasant Cove, an experimental community secretly owned by Cobra. He soon finds out that they, and the whole population of the town are brainwashed slaves of Cobra, and if captured, Flint may be joining them.
Dusty and Footloose must help Dr. Nancy Winters, a beautiful scientist who was tricked into designing a plasma cannon for Destro. She is being held by Destro's men. Dusty and Footloose decide to rescue her. They steal a vehicle from a Cobra Officer then proceed with the rescue. They meet a man named Ahmed Razouli Jabal, a king who plans on avenging the capture of his people by Cobra and liberating them from his country.
Story by: Alfred A. Pegal
G.I. Joe go underwater to find a nuclear submarine called the Nerka, and rescue a crew being held captive by Cobra. Helping in the search is Mara, a woman Shipwreck saved from drowning who has blue skin that was genetically modified by Cobra to be the first of many "aquatic commandos".
G.I. Joe designs a new armor treatment that's impenetrable to laser fire and missiles. While on leave, Dusty is desperate after seeing his mother struggle with her asthma and mounting medical bills, so he makes a deal with Extensive Enterprises' Crimson Twins to pay for the costs in return for the armor formula. He secretly informs Cobra about it, leading his team into an ambush that left Duke in a coma. Now, the Joes have a traitor in their midst.
In order to prove himself in Cobra, Dusty must battle a Cobra soldier named Lt. Claymore in the Arena of Death with man-eating pirana. G.I. Joe revamp security and launch a full-scale assault against their former comrade and Cobra to protect their armor treatment project. But when the Joes are captured by Cobra Commander to be subjects for his mind control gas, an unexpected twist of events proves that not all is what it seems.
Colonel Sharp buys an advanced computer program code-named Watchdog to be the new commander for G.I. Joe, until they discover its owned by Cobra. The program ordered Admiral Ledger on the U.S.S. Flag to attack the Cobra ship Cerebus, but it disappeared in the Indian Ocean. Now Flint, Lady Jaye, and Heavy Metal have to take out Watchdog along with its faux designer, Dr. Hamler.
Story by: Flint Dille
Cobra captures satellites to create their own television network. G.I. Joe must head into space and destroy the space station before Cobra's propaganda infects everyone in the world.
Story by: Flint Dille
Cobra devises a plot to take control of Washington D.C. and Moscow with the aid of UFO's, causing suspicion and paranoia between the U.S. and the Soviet Union. G.I. Joe and the Oktober Guard, an elite Russian combat force reluctantly join forces to stop Cobra.
After Cobra is disbanded, Destro invents a "subliminal enslavement program" to bend the will of the population to Cobra's way of thinking. In order to use the program, Cobra Commander gets Zartan and the Dreadnoks to form a rock n' roll band called "Cold Slither" to perform music with subliminal messages as part of Cobra taking control the minds of the masses. But Breaker, Footloose, and Shipwreck get caught up in the music and go to their concert, making G.I. Joe come after them and put a stop to Cobra, forming their own band called "The Average Joe Band" to please the audience.
G.I. Joe and the Oktober Guard need to locate the real Seal of Alaska before Cobra takes control of Alaska and its resources. While searching, the Joes and Red Oktober get captured by 19th-century Cossacks, who bring them to Captain Lukrov who has the great seal. But he loses it to Cobra and Duke makes a deal with Lukrov to retrieve it.
Lady Jaye receives a letter of inheritance from Dame Agatha Doyle leaving her a manor house in Loch Lomond in Northern Scotland, which turns out to be the ancestral castle of Destro. She witnesses a winter solstice ritual to raise the power of evil, and if seen, she may be forced to participate in, leaving Flint and G.I. Joe to come rescue her.
While on an island, Lady Jaye and Shipwreck are on a rescue mission to save Professor Mulaney, a scientist who claims of developing a new weapon to turn water into a bomb. When they find him, he implants the secret formula into Shipwreck's brain, which can only be released by a secret code word he gives to Lady Jay. Shipwreck passes out trying to escape after a Cobra assault and wakes up six years later in a place called Springfield, with Mara as his wife and a daughter named Alfea. G.I. Joe has won the war against Cobra, but he tries to find out how in the years he's missed.
When Shipwreck is plagued by nightmares of what happened in the past six years he's missed, but he soon discovers this might be Cobra's plan to retrieve the stored formula of Operation Hot Water from his mind. While Zartan creates G.I. Joe synthoid copies out of a material called pseudoplasm to look like the real thing. Knowing something is amiss when he realizes he didn't age, Shipwreck calls the Joes to Temple Alpha, Springfield's true area, and they plan to take down Cobra once and for all.
As G.I. Joe sets up their base of operations on the U.S.S. Flagg, on Delta Space Station, Dusty and Mutt warn the team about Cobra's plan to plant cubes at strategic locations in order to create the pyramid of darkness. Shipwreck and Snake Eyes travel underneath Enterprise City with secret control cubes, while the rest of the Joes plans to stop Destro from activating the first cube at the "Devil's Playground".
Tomax is captured by G.I. Joe, causing his identical twin brother Xamot to plan on rescuing him before Cobra can activate the final cube in the "Sea of Lost Souls". Shipwreck and Snake Eyes find an ally in a pop singer named "Satin", who helps them escape Cobra's troopers in Enterprise City.
Cobra activates the Pyramid of Darkness, leaving the Joes stranded at sea. The Crimson Twins anticipate Cobra Commander's treachery and signal for the Dreadnoks to relieve Zartan and Cobra Commander of control. Alpine and Bazooka ally with Quick Kick, a stuntman and karate expert from Hollywood.
G.I. Joe regains control of Space Station Delta, and they launch a full-scale assault on Cobra Temple, destroying the control cubes and the Pyramid of Darkness.
Cobra tries to attack a global anti-terrorism conference when they send Zartan to replace an ambassador and blow up the Worldwide Defense Center, but G.I. Joe captures and places him in the Defense Center's prison.
Roadblock's aunt and uncle run a fast food place called Red Rocket owned by Extensive Enterprises, Cobra's business alias. The rocket design hides extremely destructive warheads that Cobra hopes to utilize. G.I. Joe goes on a countrywide search for Red Rocket restaurants with Cobra missiles.
A military satellite crashes into the South Pacific, causing a race between G.I. Joe and Cobra to gain possession of it. A primitive tribe finds it first, claiming it as their god.
Cobra uses a cloaking device to make oil tankers disappear so they can detonate them by remote in an effort to take control of the world's fuel supply, unless G.I. Joe can stop the bombings.
In a plan to attack the world's cities with lava, Dr. Shakur, a scientist who invented the Vulcan Machine, is captured by Cobra. G.I. Joe must head into Cobra's jungle base, rescue the doctor and stop Cobra from carrying out their mission before these cities literally become "hotspots".
Cobra uses a special weapon called "Hi-Freq" given to them by an evil scientist named Dr. Lucifer, which a mind control device that takes over all animals in the animal kingdom, including Mutt's dog Junkyard. G.I. Joe has to stop Cobra's Hi-Freq device and save every animal in the world, especially Junkyard who isn't man's best friend, but Mutt's worst enemy.
Several scientists have been captured by Cobra and imprisoned in South America, prompting the Joes to rescue them and go through Cobra's booby-trapped "funhouse".
The Joes discover Cobra's plan to invade the Rocky Mountain Chemical Weapons Arsenal to possess explosive gas, all while under scrutiny from Hector Ramirez, host of the television show Twenty Questions.
A top secret nitrogen rocket fuel is stolen from the Joes and is accidentally stored in a greenhouse. The plants grow immensely, giving Destro a plan to seed the world with mutated fruits and vegetables to crush G.I. Joe in this gigantic jungle.
Cobra creates a weapon called the "Ion Attractor" that can pull down the Aurora Borealis to melt the polar icecaps and flood the world. G.I. Joe and a group of scientists must head north to prevent a global disaster.
Zartan makes constructs called synthoids, artificial beings or life forms loyal only to Cobra. Cobra makes Synthoids of Admiral Ledger, Colonel Sharp, General Franks, General Howe, and Duke to cut off G.I. Joe's resources and undermine morale.
Betrayed by an impostor in their ranks, G.I. Joe is disbanded by the government. Now fugitives from the military, the Joes must ally with Destro who gives them information on how to defeat Cobra Commander and Zartan to regain their resources.
Cobra Commander and the Baroness hire a Gypsy to summon three ghosts; a Centurion warrior, a Mongolian Amazon, and a World War I American pilot ace, to destroy G.I. Joe. The Baroness informs the Joes to locate a Roman coin, a wedding ring, and heart-shaped locket from Cobra Commander, and then bury the items to make the ghosts disappear.
Cobra Commander's personal Firebat with a homing signal was located at a Hollywood studio for a filming of "The G.I. Joe Story". Cobra hires Zartan and the Dreadnoks to recapture the Firebat before G.I. Joe can discover it and use the homing device to attack Cobra headquarters.
A sleazy political candidate hires Cobra to cause trouble for his opponent Robert Harper during their mayoral campaign race. They keep sending gang members to harass and ruin his campaign. But G.I. Joe is sent in to restore law and order.
Cobra invents a molecular degenerator to disrupt all U.S. currency, allowing them to mint their own Cobra money. The Joes must destroy the machine before Cobra can takes over the world with the face of Cobra Commander on every paper money.
Cobra captures people with psionic abilities in order to exploit their powers to rule the world and one of them is Airborne's telekinetic little brother.
Cobra steals all the gold bars from Fort Knox and loads it inside a bullet train. G.I. Joe plans on stopping the Cobra Bullet before it reaches the coast.
Cobra develops a powerful sound weapon and attacks a Sheik's oil supply with it in the Middle East. G.I. Joe must stop Cobra before they leak oil everywhere.
Wild Bill and a few Joes head to a farm in Texas to investigate a dude ranch Cobra captured, near the solar panels in order to control a nearby power station.
A twisted tycoon captures Flint, Lady Jaye, Baroness, and Cobra Commander, who must work together to escape the life size toys that are attacking them.
The Baroness spies on the Joes to gain access to the laser guidance system for Cobra Commander. While giving a martial art demonstration, Quick Kick meets Amber, a college student who dreams of being a Joe. They pair soon date and as his girlfriend, Amber gets closer to the Joes secrets, which causes them to think she is a Cobra spy.
Cobra steals a dangerous bacteria which causes a strong bacterium and growth serum to form a living germ monster that consumes everything in its path.
At his fire station, Barbecue keeps getting phone calls with cryptic messages from a man who calls himself "The Viper" and enlists the rest of the Joes to help him catch this mysterious man.
The Baroness uses the song of the Sirens to put the males under her evil spell. With their comrades under the Baroness' control, Cover Girl, Lady Jaye, and Scarlett are the only ones who can stop her and set their hypnotized friends free.
In an attempt to stop a world financial summit, Cobra heads to Japan to cause an artificially created earthquake that will destroy Tokyo unless G.I. Joe can stop their plans.
Cobra kidnaps family members of several G.I. Joe members and brainwashes them to obey the Baroness' commands. The Baroness commands the captives to attack the Joes in her attempt to retrieve the explosive crystals that Cobra created.
Scarlett and the other Joes set out to find a way to free their families from the Baroness' control. Unfortunately, the Baroness wants possession of the crystals and she would stop at nothing to get what she wants.
While camping, Bazooka sees a Cobra flight pod get "eaten" by a giant sea serpent. In reality, this "sea serpent" is a Cobra submarine planning to steal everything it devours. But when it goes out of control, the sea serpent goes on a rampage and the Joes must stop it from destroying New York.
G.I. Joe sets up a radar tracking station in England. While Storm Shadow finds King Arthur's legendary sword Excalibur at the bottom of a lake and uses its strength to attack the Joes and destroy their station.
During a struggle between G.I. Joe and Cobra, an accident triggers an experimental weapon. The Joes are plunged into unconsciousness. When they awaken, the explosion hurls them into an alternate reality, where Washington, D.C. and the rest of the world are under the control of Cobra.
While stuck in the alternate world, the Joes find an unlikely ally, the Baroness. Steeler learns that the Baroness of this world is a double agent and his beloved. She helps rescue the Joes and sends them back to their own home world. But Steeler, Clutch, and Grunt decide to stay in the other world after seeing what Cobra had done to their alternate selves.
Destro concocts a love potion out of Cleopatra's perfume for the Baroness to make a wealthy shipping tycoon fall in love with her. But things turn awry when Lady Jaye is sprayed with the scent.
Story by: Dann Thomas and Roy Thomas
It's Christmas Eve and most of the Joes have gone home for the holidays. After using special growth/shrinking ray and special toys (similar to the Trojan Horse) slipped into the donated toys for charity, Cobra ends up successfully infiltrating the G.I. Joe Headquarters, captures the Joes present, and rewires the Joes equipment. They plan on attacking Keystone City on Christmas to have residents believe the Joes have turned treacherous against them.
While in the midst of transporting valuables, G.I. Joe gets ambushed by Cobra, causing them to accidentally set a remote cabin in the mountains on fire. This makes the cabin's owner, Charlie Fairmont demand retribution against Cobra and Lady Jaye helps him with his revenge.
Gordon Kent
Cobra heads for Egypt to steal the treasure of Osiris in an underground tomb. G.I. Joe find themselves facing him and the Egyptian gods while Cobra faces Set, the Egyptian god of evil.
Cobra steals dinosaur bones and kidnaps a biologist to have him recreate the dinosaurs in a cloning device with rapid growth serum in order to destroy G.I. Joe and rule the world.
Flint visits his cousins in Pleasant Cove, an experimental community secretly owned by Cobra. He soon finds out that they, and the whole population of the town are brainwashed slaves of Cobra, and if captured, Flint may be joining them.
Dusty and Footloose must help Dr. Nancy Winters, a beautiful scientist who was tricked into designing a plasma cannon for Destro. She is being held by Destro's men. Dusty and Footloose decide to rescue her. They steal a vehicle from a Cobra Officer then proceed with the rescue. They meet a man named Ahmed Razouli Jabal, a king who plans on avenging the capture of his people by Cobra and liberating them from his country.
Story by: Alfred A. Pegal
G.I. Joe go underwater to find a nuclear submarine called the Nerka, and rescue a crew being held captive by Cobra. Helping in the search is Mara, a woman Shipwreck saved from drowning who has blue skin that was genetically modified by Cobra to be the first of many "aquatic commandos".
G.I. Joe designs a new armor treatment that's impenetrable to laser fire and missiles. While on leave, Dusty is desperate after seeing his mother struggle with her asthma and mounting medical bills, so he makes a deal with Extensive Enterprises' Crimson Twins to pay for the costs in return for the armor formula. He secretly informs Cobra about it, leading his team into an ambush that left Duke in a coma. Now, the Joes have a traitor in their midst.
In order to prove himself in Cobra, Dusty must battle a Cobra soldier named Lt. Claymore in the Arena of Death with man-eating pirana. G.I. Joe revamp security and launch a full-scale assault against their former comrade and Cobra to protect their armor treatment project. But when the Joes are captured by Cobra Commander to be subjects for his mind control gas, an unexpected twist of events proves that not all is what it seems.
Colonel Sharp buys an advanced computer program code-named Watchdog to be the new commander for G.I. Joe, until they discover its owned by Cobra. The program ordered Admiral Ledger on the U.S.S. Flag to attack the Cobra ship Cerebus, but it disappeared in the Indian Ocean. Now Flint, Lady Jaye, and Heavy Metal have to take out Watchdog along with its faux designer, Dr. Hamler.
Story by: Flint Dille
Cobra captures satellites to create their own television network. G.I. Joe must head into space and destroy the space station before Cobra's propaganda infects everyone in the world.
Story by: Flint Dille
Cobra devises a plot to take control of Washington D.C. and Moscow with the aid of UFO's, causing suspicion and paranoia between the U.S. and the Soviet Union. G.I. Joe and the Oktober Guard, an elite Russian combat force reluctantly join forces to stop Cobra.
After Cobra is disbanded, Destro invents a "subliminal enslavement program" to bend the will of the population to Cobra's way of thinking. In order to use the program, Cobra Commander gets Zartan and the Dreadnoks to form a rock n' roll band called "Cold Slither" to perform music with subliminal messages as part of Cobra taking control the minds of the masses. But Breaker, Footloose, and Shipwreck get caught up in the music and go to their concert, making G.I. Joe come after them and put a stop to Cobra, forming their own band called "The Average Joe Band" to please the audience.
G.I. Joe and the Oktober Guard need to locate the real Seal of Alaska before Cobra takes control of Alaska and its resources. While searching, the Joes and Red Oktober get captured by 19th-century Cossacks, who bring them to Captain Lukrov who has the great seal. But he loses it to Cobra and Duke makes a deal with Lukrov to retrieve it.
Lady Jaye receives a letter of inheritance from Dame Agatha Doyle leaving her a manor house in Loch Lomond in Northern Scotland, which turns out to be the ancestral castle of Destro. She witnesses a winter solstice ritual to raise the power of evil, and if seen, she may be forced to participate in, leaving Flint and G.I. Joe to come rescue her.
While on an island, Lady Jaye and Shipwreck are on a rescue mission to save Professor Mulaney, a scientist who claims of developing a new weapon to turn water into a bomb. When they find him, he implants the secret formula into Shipwreck's brain, which can only be released by a secret code word he gives to Lady Jay. Shipwreck passes out trying to escape after a Cobra assault and wakes up six years later in a place called Springfield, with Mara as his wife and a daughter named Alfea. G.I. Joe has won the war against Cobra, but he tries to find out how in the years he's missed.
When Shipwreck is plagued by nightmares of what happened in the past six years he's missed, but he soon discovers this might be Cobra's plan to retrieve the stored formula of Operation Hot Water from his mind. While Zartan creates G.I. Joe synthoid copies out of a material called pseudoplasm to look like the real thing. Knowing something is amiss when he realizes he didn't age, Shipwreck calls the Joes to Temple Alpha, Springfield's true area, and they plan to take down Cobra once and for all.